SAXSdb — 8urq

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Meiotic recombination protein REC104

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 1	Meiotic recombination protein REC102 × 1 （Q02721） Meiosis-specific protein SPO11 × 1 （P23179） Antiviral protein SKI8 × 1 （Q02793） gapped DNA × 1 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RE104_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain F； PDBConstruct 1–182； UniProt 1–182

Meiotic recombination protein REC102

Saccharomyces cerevisiae S288C

UniProt Q02721

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 1	Meiotic recombination protein REC104 × 1 （P33323） Meiosis-specific protein SPO11 × 1 （P23179） Antiviral protein SKI8 × 1 （Q02793） gapped DNA × 1 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TO6BL_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–264； UniProt 1–264

Meiosis-specific protein SPO11

Saccharomyces cerevisiae S288C

UniProt P23179

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 1	Meiotic recombination protein REC104 × 1 （P33323） Meiotic recombination protein REC102 × 1 （Q02721） Antiviral protein SKI8 × 1 （Q02793） gapped DNA × 1 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPO11_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–398； UniProt 1–398

Antiviral protein SKI8

Saccharomyces cerevisiae S288C

UniProt Q02793

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 1	Meiotic recombination protein REC104 × 1 （P33323） Meiotic recombination protein REC102 × 1 （Q02721） Meiosis-specific protein SPO11 × 1 （P23179） gapped DNA × 1 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SKI8_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–397； UniProt 1–397

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8urq
Deposition date deposition_date	2023-10-26
Structure title title	Spo11 core complex with gapped DNA
Keywords keywords	Spo11, Rec102, Rec104, Ski8, DNA binding, Cross over., DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8urq__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8urq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8urq__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	37.92 Å
Rg (electron density)	38.44 Å
Total Rg	38.68 Å
Atom count	8569
Residues	1024
Excluded volume	151130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8urq__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Meiotic recombination protein REC104
Molecular weight formula_weight	20763.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F
Atom count atom_count	8569

MSIEEEDTNKITCTQDFLHQYFVTERVSIQFGLNNKTVKRINKDEFDKAVNCIMSWTNYPKPGLKRTASTYLLSNSFKKSATVSLPFILGDPVCMPKRVESNNNDTCLLYSDTLYDDPLIQRNDQAGDEIEDEFSFTLLRSEVNEIRPISSSSTAQILQSDYSALMYERQASNGSIFQFSSP

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Meiotic recombination protein REC102
Molecular weight formula_weight	30263.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MARDITFLTVFLESCGAVNNDEAGKLLSAWTSTVRIEGPESTDSNSLYIPLLPPGMLKIKLNFKMNDRLVTEEQELFTKLREIVGSSIRFWEEQLFYQVQDVSTIENHVILSLKCTILTDAQISTFISKPRELHTHAKGYPEIYYLSELSTTVNFFSKEGNYVEISQVIPHFNEYFSSLIVSQLEFEYPMVFSMISRLRLKWQQSSLAPISYALTSNSVLLPIMLNMIAQDKSSTTAYQILCRRRGPPIQNFQIFSLPAVTYNK

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Meiosis-specific protein SPO11
Molecular weight formula_weight	50020.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MALEGLRKKYKTRQELVKALTPKRRSIHLNSNGHSNGTPCSNADVLAHIKHFLSLAANSLEQHQQPISIVFQNKKKKGDTNSPDIHTTLDFPLNGPHLSTHQFKLKRCAILLNLLKVVMEKLPLGKNTTVRDIFYSNVELFQRQANVVQWLDVIRFNFKLSPRKSLNIIPAQKGLVYSPFPIDIYDNILTCENEPKMQKQTIFSGKPCLIPFFQDDAVIKLGTTSMCNIVIVEKEAVFTKLVNNYHKLSTNTMLITGKGFPDFLTRLFLKKLEQYCSNLISDCSIFTDADPYGISIALNYTHSNERNAYICTMANYKGIRITQVLAQNNEVHNKSIQLLSLNQRDYSLAKNLIASLTANSWDIATSPLKNVVIECQREIFFQKKAEMNEIDAGIFKYKSRHHHHHHHHHHGDYKDDDDKDYKDDDDKDYKDDDDK

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

Entity 4 Entity 4 polymer

Description description	Antiviral protein SKI8
Molecular weight formula_weight	44313.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSKVFIATANAGKAHDADIFSVSACNSFTVSCSGDGYLKVWDNKLLDNENPKDKSYSHFVHKSGLHHVDVLQTIERDAFELCLVATTSFSGDLLFYRITREDETKKVIFEKLDLLDSDMKKHSFWALKWGASNDRLLSHRLVATDVKGTTYIWKFHPFADESNSLTLNWSPTLELQGTVESPMTPSQFATSVDISERGLIATGFNNGTVQISELSTLRPLYNFESQHSMINNSNSIRSVKFSPQGSLLAIAHDSNSFGCITLYETEFGERIGSLSVPTHSSQASLGEFAHSSWVMSLSFNDSGETLCSAGWDGKLRFWDVKTKERITTLNMHCDDIEIEEDILAVDEHGDSLAEPGVFDVKFLKKGWRSGMGADLNESLCCVCLDRSIRWFREAGGK

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

Entity 5 Entity 5 polymer

Description description	gapped DNA
Molecular weight formula_weight	21943.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TAGGCCGTCGGCTACTAAAAGTAGCCGACGGCCGGATTAGCAATGTAATCGTCTTAAGACGATTACATTGC

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	548674

Spo11 core complex with gapped DNA

1. Protein Identity and Related Structures Protein Identity & Related Structures

Meiotic recombination protein REC104

State in the Current Structure

Other States of the Same Protein in the Database

Meiotic recombination protein REC102

State in the Current Structure

Other States of the Same Protein in the Database

Meiosis-specific protein SPO11

State in the Current Structure

Other States of the Same Protein in the Database

Antiviral protein SKI8

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8urq__assembly_1__model_1

8urq__assembly_1__model_1 | I(q)

8urq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)

Spo11 core complex with gapped DNA

1. Protein Identity and Related Structures Protein Identity & Related Structures

Meiotic recombination protein REC104

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Meiotic recombination protein REC102

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Meiosis-specific protein SPO11

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Antiviral protein SKI8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8urq__assembly_1__model_1

8urq__assembly_1__model_1 | I(q)

8urq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)